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Full-Text Articles in Computational Biology
A Novel Pathway-Based Distance Score Enhances Assessment Of Disease Heterogeneity In Gene Expression, Yunqing Liu, Xiting Yan
A Novel Pathway-Based Distance Score Enhances Assessment Of Disease Heterogeneity In Gene Expression, Yunqing Liu, Xiting Yan
Yale Day of Data
Distance-based unsupervised clustering of gene expression data is commonly used to identify heterogeneity in biologic samples. However, high noise levels in gene expression data and the relatively high correlation between genes are often encountered, so traditional distances such as Euclidean distance may not be effective at discriminating the biological differences between samples. In this study, we developed a novel computational method to assess the biological differences based on pathways by assuming that ontologically defined biological pathways in biologically similar samples have similar behavior. Application of this distance score results in more accurate, robust, and biologically meaningful clustering results in both …
Exploring The Ipf Lung Through The Lens Of Single Cell Rna Sequencing, Taylor Adams, Jonas Schupp
Exploring The Ipf Lung Through The Lens Of Single Cell Rna Sequencing, Taylor Adams, Jonas Schupp
Yale Day of Data
This poster illustrates the differences between the IPF disease-specific variety of lung macrophages and the two varieties of macrophages known to reside in the normal human lung.
Penetrance Estimates For Incidental Genomic Findings In Acmg-59, James A. Diao
Penetrance Estimates For Incidental Genomic Findings In Acmg-59, James A. Diao
Yale Day of Data
The dropping costs and rising popularity of next-generation sequencing has introduced the possibility of personalizing medical treatments and screening for genetic diseases. Still, the clinical community’s understanding remains incomplete, with limited consensus on the proper interpretation for many genetic variants. Thus, the standard procedure when returning sequencing results has been to report findings only in genes related to the diagnostic indication, and not incidental findings in other genes. To balance the threat of false positives with the medical benefits of true findings, the American College on Medical Genetics and Genomics (ACMG) recommends an exception: that clinical sequencing laboratories seek and …
Detecting Modules In Multiplex Networks – An Application For Integrating Expression Profiles Across Multiple Species, Koon-Kiu Yan, Daifeng Wang, Joel Rozowsky, Henry Zheng, Baikang Pei, Mark Gerstein
Detecting Modules In Multiplex Networks – An Application For Integrating Expression Profiles Across Multiple Species, Koon-Kiu Yan, Daifeng Wang, Joel Rozowsky, Henry Zheng, Baikang Pei, Mark Gerstein
Yale Day of Data
Multiplex network, a set of networks linked through interconnected layers, is a useful mathematical framework for data integration. Here, we present a general method to detect modules in multiplex networks and apply it in a specific biological context: to simultaneously cluster the genome-wide expression profiles of C. elegans and D. melanogaster generated by the ENOCDE and modENCODE consortia. The method revealed modules that are fundamentally cross-species and can either be conserved or species-specific. In general, the method could be applied in various contexts like the integration of different social networks.